Differential transcriptome analysis of murine embryonic and lung fibroblasts in response to SHH pathway activation

Purpose: To identify differential mRNA expression in response to SHH stimulation in murine embryonic and lung fibroblasts Methods: NIH-3T3 and MLg cell lines were treated with recombinant SHH or vehicle control and RNA-seq was performed using Illumina Miseq Nano (performed by Admera Health, LLC (South Plainfield, NJ)). The FASTQ files were checked for quality using FastQC (v0.11.2). FASTQ files were mapped to the mm10 assembly of the mouse genome using TopHat; fragments per kilo base per million mapped reads (FPKM) calculation and differential expression analysis were performed using Cufflinks (v 2.2.1). Results: Comparison of differentially up-regulated and down-regulated mRNAs of secretory protein genes in NIH-3T3 and MLg cell lines upon SHH activation revealed interesting differences in the production of some ligands. Overall design: Embryonic (NIH-3T3) and lung fibroblasts (MLg) cell lines were treated with SHH recombinant protein or vehicle control and RNAseq was performed to identify and compare differentially up-regulated and down-regulated genes of